U.S. flag

An official website of the United States government

Ag Data Commons Maintenance - Friday 03/31/23

The Ag Data Commons website and application may experience brief, intermittent outages due to network issues. Avoid adding or editing datasets during this period to prevent losing information.. We apologize for the inconvenience. This notice will be removed once the issue is resolved.

License

U.S. Public Domain
[Open Data]

Other Access

The information on this page (the dataset metadata) is also available in these formats:

JSON RDF

via the DKAN API

Data Extent

Social

Data from: Draft Genome Assembly of Passalora sequoiae a Needle Blight Pathogen on Leyland Cypress

The objective was to generate a high-quality draft assembly of the whole genome as a resource for future applications such as temporal and spatial dispersal studies of the pathogen and to investigate genotype diversity relevant in fungicide resistance studies and cypress breeding programs. We report here the genome sequence of Passalora sequoiae 9LC2 that was isolated from Leyland cypress 'Leighton Green' (Cupressocyparis leylandii) in 2017 in southern Mississippi. The draft genome was obtained using Pacific Biosciences (PacBio) SMRT and Illumina HiSeq 2500 sequencing. Illumina reads were mapped to PacBio assembled contigs to determine base call consistency. Based on a total of 44 contigs with 722 kilobase (kb) average length (range 9.4 kb to 3.4 Mb), the whole genome size was estimated at 31,768,716 bp. Mapping of Illumina reads to PacBio contigs resulted in a 1000 x coverage and were used to confirm accuracy of the consensus sequences.

The figures and methods files are documentation in support of a BMC Data Notes publication 'Draft Genome Assembly of Passalora sequoiae a Needle Blight Pathogen on Leyland Cypress'. The images illustrate

  • Leyland cypress tree showing Passalora twig blight symptoms
  • Infected Leyland cypress leaf with sporulating conidioma of Passalora sequoiae
  • Conidia of Passalora sequoiae
  • Passalora 9LC2 phylogeny

.

See all >>
FieldValue
Tags
NP305
Modified
2022-01-05
Release Date
2020-06-18
Identifier
4585d67b-12f8-4722-a804-772e2afb2180
Spatial / Geographical Coverage Area
POLYGON ((-88.471115 34.995703, -88.202745 34.995703, -88.098683 34.891641, -88.241084 33.796253, -88.471115 31.895754, -88.394438 30.367688, -88.503977 30.323872, -88.744962 30.34578, -88.843547 30.411504, -89.084533 30.367688, -89.418626 30.252672, -89.522688 30.181472, -89.643181 30.285534, -89.681519 30.449842, -89.845827 30.66892, -89.747242 30.997536, -91.636787 30.997536, -91.565587 31.068736, -91.636787 31.265906, -91.516294 31.27686, -91.499863 31.643815, -91.401278 31.621907, -91.341032 31.846462, -91.105524 31.988862, -90.985031 32.218894, -91.006939 32.514649, -91.154816 32.640618, -91.143862 32.843265, -91.072662 32.887081, -91.16577 33.002096, -91.089093 33.13902, -91.143862 33.347144, -91.056231 33.429298, -91.231493 33.560744, -91.072662 33.867453, -90.891923 34.026284, -90.952169 34.135823, -90.744046 34.300131, -90.749522 34.365854, -90.568783 34.420624, -90.585214 34.617794, -90.481152 34.661609, -90.409952 34.831394, -90.251121 34.908072, -90.311367 34.995703, -88.471115 34.995703))
Publisher
Ag Data Commons
Temporal Coverage
January 1, 2017 to December 31, 2017
License
U.S. Public Domain
Contact Name
Copes, Warren
Contact Email
warren.copes@usda.gov
Public Access Level
Public
Program Code
005:040 - Department of Agriculture - National Research
Bureau Code
005:18 - Agricultural Research Service
Extended Metadata: 
FieldValue
Authors
Copes, Warren (ORCID)
Caballero, Jorge I. (Scopus Author ID)
Babiker, Ebrahiem (ORCID)
Stewart, Jane E. (ORCID)
Orner, Valerie A. (Scopus Author ID)
Windham, Alan S. (Scopus Author ID)
Arias, Renee S. (ORCID)
Peer Reviewed
No
Intended Use
To generate a high-quality draft assembly of the whole genome as a resource for future applications such as temporal and spatial dispersal studies of the pathogen and to investigate genotype diversity relevant in fungicide resistance studies and cypress breeding programs.
Funding Sources
Agricultural Research Service
6404-21430-001-00D
Primary Article

Copes, W. E., Ibarra Caballero, J., Babiker, E., Stewart, J. E., Orner, V. A., Windham, A. S., & Arias, R. S. (2020). Draft genome assembly of Passalora sequoiae a needle blight pathogen on Leyland cypress. BMC Research Notes, 13(1). https://doi.org/10.1186/s13104-020-05328-3
Dataset DOI (digital object identifier)
10.15482/USDA.ADC/1518905
Related Content
Passalora sequoiae isolate 9LC2, whole genome shotgun sequencing project - GenBank Accession WSQC00000000
FieldValue
ARIS Log Number
374084
OSTI Identifier
ISO Topic(s)
biota
State or Territory
Mississippi
National Agricultural Library Thesaurus Term
genome assembly
Passalora sequoiae
blight
pathogens
Cupressocyparis leylandii
genome
genotype
fungicide resistance
breeding
nucleotide sequences
Mississippi
Ag Data Commons Keywords
  • Genomics & Genetics
  • Genome
  • Genome assembly
  • Genomics & Genetics
  • Genome
  • Genome annotation
  • Genomics & Genetics
  • Genome
  • Genomics & Genetics
  • Plants & Crops
  • Plant health
  • Plants & Crops
  • Agroecosystems & Environment
  • Agricultural pests
  • Agroecosystems & Environment

Suggested Citations:

(original article) Copes, W. E., Ibarra Caballero, J., Babiker, E., Stewart, J. E., Orner, V. A., Windham, A. S., & Arias, R. S. (2020). Draft genome assembly of Passalora sequoiae a needle blight pathogen on Leyland cypress. BMC Research Notes, 13(1). https://doi.org/10.1186/s13104-020-05328-3

(dataset) Copes, Warren; Caballero, Jorge I.; Babiker, Ebrahiem; Stewart, Jane E.; Orner, Valerie A.; Windham, Alan S.; Arias, Renee S. (2020). Data from: Draft Genome Assembly of Passalora sequoiae a Needle Blight Pathogen on Leyland Cypress. Ag Data Commons. https://doi.org/10.15482/USDA.ADC/1518905. Accessed 2023-04-01.